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Pyclone on HPC

PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. The input data for PyClone consists of a set read counts from a deep sequencing experiment, the copy number of the genomic region containing the mutation and an estimate of tumour content.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pyclone
[user@cn3144 ~]$ PyClone analyse config.yaml

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load pyclone
PyClone analyse config.yaml

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. job.swarm). For example:

cd dir1;PyClone analyse config.yaml
cd dir2;PyClone analyse config.yaml
cd dir3;PyClone analyse config.yaml
cd dir4;PyClone analyse config.yaml

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module pyclone
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm